Inside, the nave ceiling is frescoed with a Glory of St John the Baptist by Dionisio Montorselli.
The nave walls have fifteen frescoes by diverse artists, depicting events in the Life of John the Baptist.
The painters include Dionisio Montorselli (Annuciation), Rutilio Manetti (4 canvases including the main altarpiece of the Baptism of Christ, John the Baptist declares Christ to the Pharisees), Domenico Manetti, Giovan Battista Giustammiani, called il Francesino, (Burial of John the Baptist) Bernardino Mei (Decapitation of the Baptist) ; Raffaello Vanni (St Zacharius at the Temple), Deifebo Burbarini (St Francis), and Astolfo Petrazzi (Decapitation of Sts John and Ansano).
Some works have been attributed to Angelo di Niccolò Tegliacci (Baptist led to Prison), Cristoforo Rustici, Niccolo Nasini, and Tornioli (Banquet of Herod).
The vestibule of the church has a terracotta statue of the Baptist by Guidoccio Cozzarelli and a canvas of the Glory of St Joseph by Deifebo Burbarini.